Origin IGS: catctctgattttttcctaatttccaaaaatttttagtaaaatttaagatatcaattcaaatttgtgctacaatagaaaacgtgaacttttaagaataaggagtcaatataaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttatattgactccttattcttaaaagttcacgttttctattgtagcacaaatttgaattgatatcttaaattttactaaaaatttttggaaattaggaaaaaatcagagatg Mask Tandem Repeat Region ================================================ catctctgattttttcctaatttccaaaaatttttagtaaaatttaagatatcaattcaaatttgtgctacaatagaaaacgtgaacttttaagaataaggagtcaatataaa Find is-nt database================================================ Query_seq: SSA_0752:SSA_0753|SSA_0752:SSA_0753:hypothetical protein:Foldase protein prsA precursor, putative:->->:734995..735107 113 catctctgattttttcctaatttccaaaaatttttagtaaaatttaagatatcaattcaaatttgtgctacaatagaaaacgtgaacttttaagaataaggagtcaatataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0752:SSA_0753|SSA_0752:SSA_0753:hypothetical protein:Foldase protein prsA precursor, putative:->->:734995..735107 113 catctctgattttttcctaatttccaaaaatttttagtaaaatttaagatatcaattcaaatttgtgctacaatagaaaacgtgaacttttaagaataaggagtcaatataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0752:SSA_0753|SSA_0752:SSA_0753:hypothetical protein:Foldase protein prsA precursor, putative:->->:734995..735107 113 catctctgattttttcctaatttccaaaaatttttagtaaaatttaagatatcaattcaaatttgtgctacaatagaaaacgtgaacttttaagaataaggagtcaatataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 catctctgattttttcctaatttccaaaaatttttagtaaaatttaagatatcaattcaaatttgtgctacaatagaaaacgtgaacttttaagaataaggagtcaatataaa Predict ORF larger than 30AA ================================================ catctctgattttttcctaatttccaaaaatttttagtaaaatttaagatatcaattcaaatttgtgctacaatagaaaacgtgaacttttaagaataaggagtcaatataaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ catctctgattttttcctaatttccaaaaatttttagtaaaatttaagatatcaattcaaatttgtgctacaatagaaaacgtgaacttttaagaataaggagtcaatataaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0752:SSA_0753|SSA_0752:SSA_0753:hypothetical protein:Foldase protein prsA precursor, putative:->->:734995..735107 113 catctctgattttttcctaatttccaaaaatttttagtaaaatttaagatatcaattcaaatttgtgctacaatagaaaacgtgaacttttaagaataaggagtcaatataaa Intra-Species Hit: Count: 1 Min: 1 Max: 113 Len: 113 Subject: NC_009009_SSA_0752_SSA_0753|hypothetical protein:Foldase protein prsA precursor, putative|POSITIVE:POSITIVE|[734995,735107]|113 HSP 1 e-value: 5.0E-58 bit: 224.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 catctctgattttttcctaatttccaaaaatttttagtaaaatttaagatatcaattcaaatttgtgctacaatagaaaacgtgaacttttaagaataaggagtcaatataaa catctctgattttttcctaatttccaaaaatttttagtaaaatttaagatatcaattcaaatttgtgctacaatagaaaacgtgaacttttaagaataaggagtcaatataaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUCUCUGAUUUUUUCCUAAUUUCCAAAAAUUUUUAGUAAAAUUUAAGAUAUCAAUUCAAAUUUGUGCUACAAUAGAAAACGUGAACUUUUAAGAAUAAGGAGUCAAUAUAAA ......((((....((((.((((..((((..((((((......))))))......((((..(((...(((...))).)))..)))).))))..)))).))))))))....... (-10.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUAUUGACUCCUUAUUCUUAAAAGUUCACGUUUUCUAUUGUAGCACAAAUUUGAAUUGAUAUCUUAAAUUUUACUAAAAAUUUUUGGAAAUUAGGAAAAAAUCAGAGAUG ..........(((.((.(((((((.((((((.((((.(((...)))...)))).))))))....(((.(((((((....)))))))..)))..))))))).))....)))... (-11.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 210 108 62 216 169 NC_009009:SSA_0134|5end_Membrane_carboxypeptidase_(penicillin-binding_protein),_putative_171990..172220_POSITIVE 198 38 2 133 97 NC_009009:SSA_2113|5end_hypothetical_protein_2116692..2116922_NEGATIVE 189 105 65 109 70 NC_009009:SSA_0045|5end_hypothetical_protein_50333..50563_POSITIVE 179 22 1 110 89 NC_009009:SSA_0882|5end_Phosphoserine_phosphatase,_putative_876903..877133_POSITIVE 177 36 3 106 74 NC_009009:SSA_1701|5end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_1692054..1692284_NEGATIVE 177 83 56 35 11 NC_009009:SSA_0125|5end_50S_ribosomal_protein_L30,_putative_116930..117160_POSITIVE 176 106 70 142 106 NC_009009:SSA_1345|5end_Bifunctional_pyrimidine_operon_transcriptional_attenuation_protein/uracil_phosphoribosyltransferase,_putative_1363879..1364109_NEGATIVE 173 74 43 82 45 NC_009009:SSA_0282|5end_Phosphotransferase_system_(PTS),_cellobiose-specific_IIA_component,_putative_274215..274445_POSITIVE 172 38 13 118 91 NC_009009:SSA_0274|5end_hypothetical_protein_269557..269787_NEGATIVE 172 45 2 88 42 NC_009009:SSA_0062|5end_Aldose_1-epimerase,_putative_63732..63962_POSITIVE 171 97 58 162 126 NC_009009:SSA_2246|5end_Competence-damage_protein,_putative_2242496..2242726_NEGATIVE 171 97 68 177 147 NC_009009:SSA_1087|5end_ABC-type_transporter_(antibiotic_resistance_protein),_ATPase_component,_putative_1104524..1104754_POSITIVE 171 82 41 228 191 NC_009009:SSA_0733|5end_hypothetical_protein_716069..716299_POSITIVE 170 103 68 136 102 NC_009009:SSA_0017|5end_Cell_shape_determining_protein_MreC,_putative_22811..23041_POSITIVE 168 26 2 210 185 NC_009009:SSA_2160|5end_Deoxyuridinetriphosphatase,_putative_2160066..2160296_NEGATIVE 168 101 63 231 200 NC_009009:SSA_2037|5end_tRNA_(Guanosine-2'-O-)-methyltransferase,_TrmH_family,_putative_2041524..2041754_NEGATIVE 167 59 20 193 156 NC_009009:SSA_0368|5end_hypothetical_protein_359274..359504_POSITIVE 166 37 4 52 25 NC_009009:SSA_0540|5end_Glycerol_uptake_facilitator_protein,_putative_534955..535185_POSITIVE 165 105 65 196 150 NC_009009:SSA_0743|5end_Transcriptional_repressor_(arginine_synthesis),_putative_725759..725989_NEGATIVE 163 18 4 48 34 NC_009009:SSA_0469|5end_Precorrin-6B_methylase_2,putative_472310..472540_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 198 38 2 111 75 NC_009009:SSA_2114|3end_Transcriptional_repressor_of_purine_operon,_putative_2116714..2116864_NEGATIVE 179 22 1 76 55 NC_009009:SSA_0881|3end_Lipoprotein,_putative_876949..877099_POSITIVE 178 78 36 111 63 NC_009009:SSA_0143|3end_Conserved_uncharacterized_protein_137880..138030_POSITIVE 172 45 2 63 17 NC_009009:SSA_0061|3end_Tagatose_1,6-diphosphate_aldolase,_putative_63787..63937_POSITIVE 168 26 2 125 100 NC_009009:SSA_2161|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160151..2160301_NEGATIVE 167 59 20 130 93 NC_009009:SSA_0367|3end_hypothetical_protein_359291..359441_POSITIVE 163 18 4 76 62 NC_009009:SSA_0468|3end_Precorrin-6y_C5,15-methyltransferase-like,_putative_472418..472568_POSITIVE 161 105 75 40 13 NC_009009:SSA_1878|3end_Conserved_uncharacterized_protein_1871943..1872093_NEGATIVE 160 83 65 21 2 NC_009009:SSA_0124|3end_30S_ribosomal_protein_S5,_putative_116996..117146_POSITIVE 157 104 81 85 61 NC_009009:SSA_1670|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_1668637..1668787_NEGATIVE 157 104 66 52 25 NC_009009:SSA_0251|3end_D-tyrosyl-tRNA(Tyr)_deacylase,_putative_244978..245128_POSITIVE 156 39 3 100 62 NC_009009:SSA_1631|3end_Sortase-like_protein,_putative_1631651..1631801_NEGATIVE 155 107 70 73 46 NC_009009:SSA_0596|3end_hypothetical_protein_587352..587502_POSITIVE 154 50 3 141 97 NC_009009:SSA_2377|3end_ABC_transporter,_permease_component_(possible_copper_exporter),_putative_2382849..2382999_POSITIVE 154 104 75 30 1 NC_009009:SSA_0613|3end_Glucosyltransferase,_putative_606633..606783_POSITIVE 153 106 61 44 2 NC_009009:SSA_0315|3end_Transcriptional_regulator,_MarR_family,_putative_310646..310796_POSITIVE 152 101 63 82 46 NC_009009:SSA_1369|3end_FmtA-like_protein,_putative_1384142..1384292_NEGATIVE 151 70 30 70 35 NC_009009:SSA_2162|3end_hypothetical_protein_2160815..2160965_POSITIVE 151 53 11 78 28 NC_009009:SSA_1133|3end_TatA,_sec-independent_protein_secretion_pathway_component,_putative_1159665..1159815_POSITIVE 147 27 2 144 112 NC_009009:SSA_0694|3end_Mutator_protein,_putative_678421..678571_POSITIVE